tbuckley/cabot-search huggingface dataset:
How covid-19 bolstered an already perverse publishing system
Authors: Jocalyn Clark
Journal: BMJ (2023)

How covid-19 bolstered an already perverse publishing systemThe pandemic turbocharged scientific publishing.While this was widely considered a collective triumph against a global threat, have the harms of pandemic publishing been overlooked? Jocalyn ClarkEric Rubin had been in charge for only three months.The editor in chief of the New England Journal of Medicine (NEJM) had come into the role with no previous editorial experience but a career in infectious disease medicine."Little did I expect my training would be so useful," he says.As soon as the news of a pneumonia-like outbreak in China reached NEJM's editors, "we made some calls to figure out what was going on, soliciting manuscripts from colleagues in Wuhan and later in Italy and the US when the epidemic spread," says Rubin.Unsolicited submissions swelled, spiking at about 200 covid related papers a day.Editors felt the pressure of workloads, but also responsibility.Richard Horton, editor of the Lancet, told the New York Times, "We feel very much that we are publishing research that is literally, day by day, guiding the national and global response to this virus.If we make a mistake in judgment about what we publish, that could have a dangerous impact on the course of the pandemic." 1 This was the first global pandemic that the scientific publishing industry had ever faced-while journals existed, no organised industry did when the 1918 flu pandemic occurred-and the first in a new digital age of internet communication and publishing.An estimated 1.5 million articles were added to the global literature in 2020-the largest single year increase in history, says Vincent Larivière, who studies bibliometrics at the University of Montreal, Canada.This peaked in April 2020, when many countries were deep into lockdown or applying heavy restrictions.
Association of Daily Step Patterns With Mortality in US Adults
Authors: Kosuke Inoue, Yusuke Tsugawa, Elizabeth Rose Mayeda, Beate Ritz
Journal: JAMA Network Open (2023)

Importance Previous studies have shown that individuals who regularly walk, particularly 8000 daily steps or more, experience lower mortality. However, little is known about the health benefits of walking intensively only a few days a week. Objective To evaluate the dose-response association between the number of days an individual takes 8000 steps or more and mortality among US adults. Design, Setting, and Participants This cohort study evaluated a representative sample of participants aged 20 years or older in the National Health and Nutrition Examination Surveys 2005-2006 who wore an accelerometer for 1 week and their mortality data through December 31, 2019. Data were analyzed from April 1, 2022, to January 31, 2023. Exposures Participants were grouped by the number of days per week they took 8000 steps or more (0 days, 1-2 days, and 3-7 days). Main Outcomes and Measures Multivariable ordinary least squares regression models were used to estimate adjusted risk differences (aRDs) for all-cause and cardiovascular mortality during the 10-year follow-up, adjusting for potential confounders (eg, age, sex, race and ethnicity, insurance status, marital status, smoking, comorbidities, and average daily step counts). Results Among 3101 participants (mean [SD] age, 50.5 [18.4] years; 1583 [51.0%] women and 1518 [49.0%] men; 666 [21.5%] Black, 734 [23.7%] Hispanic, 1579 [50.9%] White, and 122 [3.9%] other race and ethnicity), 632 (20.4%) did not take 8000 steps or more any day of the week, 532 (17.2%) took 8000 steps or more 1 to 2 days per week, and 1937 (62.5%) took 8000 steps or more 3 to 7 days per week. Over the 10-year follow-up, all-cause and cardiovascular deaths occurred in 439 (14.2%) and 148 (5.3%) participants, respectively. Compared with participants who walked 8000 steps or more 0 days per week, all-cause mortality risk was lower among those who took 8000 steps or more 1 to 2 days per week (aRD, −14.9%; 95% CI −18.8% to −10.9%) and 3 to 7 days per week (aRD, −16.5%; 95% CI, −20.4% to −12.5%). The dose-response association for both all-cause and cardiovascular mortality risk was curvilinear; the protective association plateaued at 3 days per week. Different thresholds for the number of daily steps between 6000 and 10 000 yielded similar results. Conclusions and Relevance In this cohort study of US adults, the number of days per week taking 8000 steps or more was associated with a lower risk of all-cause and cardiovascular mortality in a curvilinear fashion. These findings suggest that individuals may receive substantial health benefits by walking just a couple days a week.
Magnetic Bead Manipulation in Microfluidic Chips for Biological Application
Authors: Gaozhe Cai, Zixin Yang, Yu-Cheng Chen, Yaru Huang, Lijuan Liang, Shilun Feng, Jianlong Zhao
Journal: Cyborg and Bionic Systems (2023)

Magnetic beads manipulation in microfluidic chips is a promising research field for biological application, especially in the detection of biological targets. In this review, we intend to present a thorough and in-depth overview of recent magnetic beads manipulation in microfluidic chips and its biological application. First, we introduce the mechanism of magnetic manipulation in microfluidic chip, including force analysis, particle properties, and surface modification. Then, we compare some existing methods of magnetic manipulation in microfluidic chip and list their biological application. Besides, the suggestions and outlook for future developments in the magnetic manipulation system are also discussed and summarized.
Integrated omics analysis for characterization of the contribution of high fructose corn syrup to non-alcoholic fatty liver disease in obesity
Authors: Grigorios Papadopoulos, Aigli-Ioanna Legaki, Konstantina Georgila, Panagiotis Vorkas, Eirini Giannousi, George Stamatakis, Ioannis I. Moustakas, Maria Petrocheilou, Iryna Pyrina, Bettina Gercken, Eva Kassi, Triantafyllos Chavakis, Ioannis S. Pateras, George Panayotou, Helen Gika, Martina Samiotaki, Aristides G. Eliopoulos, Antonios Chatzigeorgiou
Journal: Metabolism (2023)
Local Recurrence After Breast-Conserving Therapy in Patients With Multiple Ipsilateral Breast Cancer: Results From ACOSOG Z11102 (Alliance)
Authors: Judy C. Boughey, Kari M. Rosenkranz, Karla V. Ballman, Linda McCall, Bruce G. Haffty, Laurie W. Cuttino, Charlotte D. Kubicky, Huong T. Le-Petross, Armando E. Giuliano, Kimberly J. Van Zee, Kelly K. Hunt, Olwen M. Hahn, Lisa A. Carey, Ann H. Partridge
Journal: Journal of Clinical Oncology (2023)

Breast-conserving therapy (BCT) is the preferred treatment for unifocal breast cancer (BC). The oncologic safety of BCT for multiple ipsilateral breast cancer (MIBC) has not been demonstrated in a prospective study. ACOSOG Z11102 (Alliance) is a phase II, single-arm, prospective trial designed to evaluate oncologic outcomes in patients undergoing BCT for MIBC.
Biomimetic natural biomaterials for tissue engineering and regenerative medicine: new biosynthesis methods, recent advances, and emerging applications
Authors: Shuai Liu, Jiang-Ming Yu, Yan-Chang Gan, Xiao-Zhong Qiu, Zhe-Chen Gao, Huan Wang, Shi-Xuan Chen, Yuan Xiong, Guo-Hui Liu, Si-En Lin, Alec McCarthy, Johnson V. John, Dai-Xu Wei, Hong-Hao Hou
Journal: Military Medical Research (2023)

Biomimetic materials have emerged as attractive and competitive alternatives for tissue engineering (TE) and regenerative medicine. In contrast to conventional biomaterials or synthetic materials, biomimetic scaffolds based on natural biomaterial can offer cells a broad spectrum of biochemical and biophysical cues that mimic the in vivo extracellular matrix (ECM). Additionally, such materials have mechanical adaptability, microstructure interconnectivity, and inherent bioactivity, making them ideal for the design of living implants for specific applications in TE and regenerative medicine. This paper provides an overview for recent progress of biomimetic natural biomaterials (BNBMs), including advances in their preparation, functionality, potential applications and future challenges. We highlight recent advances in the fabrication of BNBMs and outline general strategies for functionalizing and tailoring the BNBMs with various biological and physicochemical characteristics of native ECM. Moreover, we offer an overview of recent key advances in the functionalization and applications of versatile BNBMs for TE applications. Finally, we conclude by offering our perspective on open challenges and future developments in this rapidly-evolving field.
HiCAT: a tool for automatic annotation of centromere structure
Authors: Shenghan Gao, Xiaofei Yang, Hongtao Guo, Xixi Zhao, Bo Wang, Kai Ye
Journal: Genome biology (2023)

Abstract Significant improvements in long-read sequencing technologies have unlocked complex genomic areas, such as centromeres, in the genome and introduced the centromere annotation problem. Currently, centromeres are annotated in a semi-manual way. Here, we propose HiCAT, a generalizable automatic centromere annotation tool, based on hierarchical tandem repeat mining to facilitate decoding of centromere architecture. We apply HiCAT to simulated datasets, human CHM13-T2T and gapless Arabidopsis thaliana genomes. Our results are generally consistent with previous inferences but also greatly improve annotation continuity and reveal additional fine structures, demonstrating HiCAT’s performance and general applicability.
Solitary Fibrous Tumor of the Prostate Shown on FAPI PET/CT
Authors: Tianshuo Yang, Ronghua Zhu, Zhongying Guo, Xiaobing Niu, Weijing Tao
Journal: Clinical Nuclear Medicine (2023)

Abstract Solitary fibrous tumors are fibroblast tumors that occur mainly in the peritoneum, extremities, and pleura. Here, we report the MRI, FDG PET/CT, and FAPI PET/CT findings of a rare prostate solitary fibrous tumor. A 57-year-old man was pathologically diagnosed with a solitary fibrous tumor. To detect any systemic metastases or other primary lesions, the patient underwent FDG PET/CT and FAPI PET/CT examination sequentially. Mild FDG uptake was observed in the primary prostatic lesion, but there was a significant uptake of FAPI in the prostate. This case highlighted that FAPI PET/CT may outperform FDG PET/CT in identifying solitary fibrous tumors.
Treatment of colorectal cancer by anticancer and antibacterial effects of hemiprotonic phenanthroline-phenanthroline+ with nanomicelle delivery
Authors: Yingying Zhang, Zizhen Zhao, Jingli Li, Qinghua Wang, Zhigang Fan, Zhibo Yuan, Yixiao Feng, Ailing Fu
Journal: Asian Journal of Pharmaceutical Sciences (2023)

Colorectal cancer (CRC) is a common digestive tract tumor worldwide. Specific microorganisms, including Fusobacterium nucleatum (F. nucleatum) and Escherichia coli (E. coli), are abundant in colonic mucosa and can promote the cancer progression and malignancy. Therefore, a therapeutic strategy is proposed to deliver effective drugs to colorectum for both anticancer and antibacteria. Here we used thin-film dispersion method to encapsulate hemiprotonic phenanthroline-phenanthroline+ (ph-ph+) into nanomicelle. The results showed that the drug-loading nanomicelle had good dispersion, and the particle size was about 28 nm. In vitro assay indicated that the nanomicelle was active against CRC-related obligate and facultative anaerobes. In human CRC cells, the nanomicelle could effectively inhibit cell proliferation and induce apoptosis. In vivo distribution showed that the nanomicelle could release ph-ph+ mainly in the colorectum. In CRC model mice, the nanomicelle significantly reduced tumor number and volume, and decreased the bacteria load and colorectal inflammation. Together, the study identifies that the ph-ph+nanomicelle has the potential to apply in treating CRC, and also suggests that anticancer combined with antimicrobial therapy would be a feasible way for CRC therapy.
Implantation of hydrogel-liposome nanoplatform inhibits glioblastoma relapse by inducing ferroptosis
Authors: Zixiao Wang, Zihao Liu, Shan Wang, Xin Bing, Xiaoshuai Ji, Dong He, Min Han, Yanbang Wei, Chanyue Wang, Qian Xia, Jianqiao Yang, Jiajia Gao, Xianyong Yin, Zhihai Wang, Zehan Shang, Jiacan Xu, Tao Xin, Qian Liu
Journal: Asian Journal of Pharmaceutical Sciences (2023)

Glioblastoma is acknowledged as the most aggressive cerebral tumor in adults. However, the efficacy of current standard therapy is seriously undermined by drug resistance and suppressive immune microenvironment. Ferroptosis is a recently discovered form of iron-dependent cell death that may have excellent prospect as chemosensitizer. The utilization of ferropotosis inducer Erastin could significantly mediate chemotherapy sensitization of Temozolomide and exert anti-tumor effects in glioblastoma. In this study, a combination of hydrogel-liposome nanoplatform encapsulated with Temozolomide and ferroptosis inducer Erastin was constructed. The αvβ3 integrin-binding peptide cyclic RGD was utilized to modify codelivery system to achieve glioblastoma targeting strategy. As biocompatible drug reservoirs, cross-linked GelMA (gelatin methacrylamide) hydrogel and cRGD-coated liposome realized the sustained release of internal contents. In the modified intracranial tumor resection model, GelMA-liposome system achieved slow release of Temozolomide and Erastin in situ for more than 14 d. The results indicated that nanoplatform (T+E@LPs-cRGD+GelMA) improved glioblastoma sensitivity to chemotherapeutic temozolomide and exerted satisfactory anti-tumor effects. It was demonstrated that the induction of ferroptosis could be utilized as a therapeutic strategy to overcome drug resistance. Furthermore, transcriptome sequencing was conducted to reveal the underlying mechanism that the nanoplatform ([email protected]+GelMA) implicated in. It is suggested that GelMA-liposome system participated in the immune response and immunomodulation of glioblastoma via interferon/PD-L1 pathway. Collectively, this study proposed a potential combinatory therapeutic strategy for glioblastoma treatment.
Use of a Deep-Learning Algorithm to Guide Novices in Performing Focused Assessment With Sonography in Trauma
Authors: I-Min Chiu, Chun-Hung Richard Lin, Fei-Fei Flora Yau, Fu-Jen Cheng, Hsiu-Yung Pan, Xin-Hong Lin, Chi-Yung Cheng
Journal: JAMA Network Open (2023)

This quality improvement study compares the diagnostic quality and completion time between ultrasonography operators guided by artificial intelligence vs those without such assistance.
Targeting neuro-immune systems to achieve cardiac tissue repair following myocardial infarction: A review of therapeutic approaches from in-vivo preclinical to clinical studies
Authors: Sarah Smith, Raimondo Ascione
Journal: Pharmacology & Therapeutics (2023)

Myocardial healing following myocardial infarction (MI) toward either functional tissue repair or excessive scarring/heart failure, may depend on a complex interplay between nervous and immune system responses, myocardial ischemia/reperfusion injury factors, as well as genetic and epidemiological factors. Hence, enhancing cardiac repair post MI may require a more patient-specific approach targeting this complex interplay and not just the heart, bearing in mind that the dysregulation or modulation of just one of these systems or some of their mechanisms may determine the outcome either toward functional repair or toward heart failure. In this review we have elected to focus on existing preclinical and clinical in-vivo studies aimed at testing novel therapeutic approaches targeting the nervous and immune systems to trigger myocardial healing toward functional tissue repair. To this end, we have only selected clinical and preclinical in-vivo studies reporting on novel treatments targeting neuro-immune systems to ultimately treat MI. Next, we have grouped and reported treatments under each neuro-immune system. Finally, for each treatment we have assessed and reported the results of each clinical/preclinical study and then discussed their results collectively. This structured approach has been followed for each treatment discussed. To keep this review focused, we have deliberately omitted to cover other important and related research areas such as myocardial ischemia/reperfusion injury, cell and gene therapies as well as any ex-vivo and in-vitro studies. The review indicates that some of the treatments targeting the neuro-immune/inflammatory systems appear to induce beneficial effects remotely on the healing heart post MI, warranting further validation. These remote effects on the heart also indicates the presence of an overarching synergic response occurring across the nervous and immune systems in response to acute MI, which appear to influence cardiac tissue repair in different ways depending on age and timing of treatment delivery following MI. The cumulative evidence arising from this review allows also to make informed considerations on safe as opposed to detrimental treatments, and within the safe treatments to ascertain those associated with conflicting or supporting preclinical data, and those warranting further validation.
Re-Evaluation of Pathologic Complete Response as a Surrogate for Event-Free and Overall Survival in Human Epidermal Growth Factor Receptor 2–Positive, Early Breast Cancer Treated With Neoadjuvant Therapy Including Anti–Human Epidermal Growth Factor Receptor 2 Therapy
Authors: Pierre Squifflet, Everardo D. Saad, Sibylle Loibl, Marion T. van Mackelenbergh, Michael Untch, Priya Rastogi, Luca Gianni, Andreas Schneeweiss, Pierfranco Conte, Martine Piccart, Hervé Bonnefoi, Christian Jackisch, Valentina Nekljudova, Gong Tang, Pinuccia Valagussa, Colin Neate, Richard Gelber, Coralie Poncet, Dominik Heinzmann, Carsten Denkert, Charles E. Geyer, Javier Cortes, Valentina Guarneri, Evandro de Azambuja, David Cameron, Gustavo Ismael, Norman Wolmark, Patricia Cortazar, Marc Buyse
Journal: Journal of Clinical Oncology (2023)

Pathologic complete response (pCR) has prognostic importance and is frequently used as a primary end point, but doubts remain about its validity as a surrogate for event-free survival (EFS) and overall survival (OS) in human epidermal growth factor receptor 2 (HER2)-positive, early breast cancer.We obtained individual-patient data from randomized trials of neoadjuvant anti-HER2 therapy that enrolled at least 100 patients, had data for pCR, EFS, and OS, and a median follow-up of at least 3 years. We quantified the patient-level association between pCR (defined as ypT0/Tis ypN0) and both EFS and OS using odds ratios (ORs, with ORs >1.00 indicating a benefit from achieving a pCR). We quantified the trial-level association between treatment effects on pCR and on EFS and OS using R2 (with values above 0.75 considered as indicating strong associations).Eleven of 15 eligible trials had data for analysis (3,980 patients, with a median follow-up of 62 months). Considering all trials, we found strong patient-level associations, with ORs of 2.64 (95% CI, 2.20 to 3.07) for EFS and 3.15 (95% CI, 2.38 to 3.91) for OS; however, trial-level associations were weak, with an unadjusted R2 of 0.23 (95% CI, 0 to 0.66) for EFS and 0.02 (95% CI, 0 to 0.17) for OS. We found qualitatively similar results when grouping trials according to different clinical questions, when analyzing only patients with hormone receptor-negative disease, and when using a more stringent definition of pCR (ypT0 ypN0).Although pCR may be useful for patient management, it cannot be considered as a surrogate for EFS or OS in neoadjuvant trials of HER2-positive, operable breast cancer.
Evaluation of Survival Following Surgical Resection for Small Nonfunctional Pancreatic Neuroendocrine Tumors
Authors: Toshitaka Sugawara, Salvador Rodriguez Franco, Michael J. Kirsch, Kathryn L. Colborn, Jun Ishida, Samuele Grandi, Mohammed H. Al-Musawi, Ana Gleisner, Marco Del Chiaro, Richard D. Schulick
Journal: JAMA Network Open (2023)

Importance The number of patients with small nonfunctional pancreatic neuroendocrine tumors (NF-PanNETs) is increasing. However, the role of surgery for small NF-PanNETs remains unclear. Objective To evaluate the association between surgical resection for NF-PanNETs measuring 2 cm or smaller and survival. Design, Setting, and Participants This cohort study used data from the National Cancer Database and included patients with NF-pancreatic neuroendocrine neoplasms who were diagnosed between January 1, 2004, and December 31, 2017. Patients with small NF-PanNETs were divided into 2 groups: group 1a (tumor size, ≤1 cm) and group 1b (tumor size, 1.1-2.0 cm). Patients without information on tumor size, overall survival, and surgical resection were excluded. Data analysis was performed in June 2022. Exposures Patients with vs without surgical resection. Main Outcomes and Measures The primary outcome was overall survival of patients in group 1a or group 1b who underwent surgical resection compared with those who did not, which was evaluated using Kaplan-Meier estimates and multivariable Cox proportional hazards regression models. Interactions between preoperative factors and surgical resection were analyzed with a multivariable Cox proportional hazards regression model. Results Of the 10 504 patients with localized NF-PanNETs identified, 4641 were analyzed. These patients had a mean (SD) age of 60.5 (12.7) years and included 2338 males (50.4%). The median (IQR) follow-up time was 47.1 (28.2-71.6) months. In total, 1278 patients were in group 1a and 3363 patients were in group 1b. The surgical resection rates were 82.0% in group 1a and 87.0% in group 1b. After adjustment for preoperative factors, surgical resection was associated with longer survival for patients in group 1b (hazard ratio [HR], 0.58; 95% CI, 0.42-0.80; P &amp;amp;lt; .001) but not for patients in group 1a (HR, 0.68; 95% CI, 0.41-1.11; P = .12). In group 1b, interaction analysis found that age of 64 years or younger, absence of comorbidities, treatment at academic institutions, and distal pancreatic tumors were factors associated with increased survival after surgical resection. Conclusions and Relevance Findings of this study support an association between surgical resection and increased survival in select patients with NF-PanNETs measuring 1.1 to 2.0 cm who were younger than 65 years, had no comorbidities, received treatment at academic institutions, and had tumors of the distal pancreas. Future investigations of surgical resection for small NF-PanNETs that include the Ki-67 index are warranted to validate these findings.
A novel lotion formulation of 20% oxybutynin hydrochloride for the treatment of primary palmar hyperhidrosis: A randomized, placebo-controlled, double-blind, phase III study
Authors: Tomoko Fujimoto, Takaaki Terahara, Koji Okawa, Hiroshi Inakura, Yuta Hirayama, Hiroo Yokozeki
Journal: Journal of the American Academy of Dermatology (2023)